Ryu, H., Han, H., Kim, C., & Kim, J. (2025). GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms. Nucleic Acids Research, 53(2), gkae1295.
@article{gkae1295,
author = {Ryu, Hyunwoo and Han, Hyunho and Kim, Chuna and Kim, Jun},
title = {GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms},
journal = {Nucleic Acids Research},
volume = {53},
number = {2},
pages = {gkae1295},
year = {2025},
month = jan,
issn = {1362-4962},
doi = {10.1093/nar/gkae1295},
file = {gkae1295.pdf},
eprint = {https://academic.oup.com/nar/article-pdf/53/2/gkae1295/61737279/gkae1295.pdf}
}
Large genetic variants can be generated via homologous recombination (HR), such as polymerase theta-mediated end joining (TMEJ) or single-strand annealing (SSA). Given that these HR-based mechanisms leave specific genomic signatures, we developed GDBr, a genomic signature interpretation tool for DNA double-strand break repair mechanisms using high-quality genome assemblies. We applied GDBr to a draft human pangenome reference. We found that 78.1% of non-repetitive insertions and deletions and 11.0% of non-repetitive complex substitutions contained specific signatures. Of these, we interpreted that 98.7% and 1.3% of the insertions and deletions were generated via TMEJ and SSA, respectively, and all complex substitutions via TMEJ. Since population-level pangenome datasets are being dramatically accumulated, GDBr can provide mechanistic insights into how variants are formed. GDBr is available on GitHub at https://github.com/Chemical118/GDBr.